I think the rematerialization thing is explainable. Jack's hand did stay in the other gate room in "Shades of Grey" -- he walked full-bore through the event horizon, then probably stopped himself from fully coming through on the other side. He held his hand in the E.H. at the S.G.C. So the matter was transmitted, but not yet fully reconstituted, preventing the rogues from being able to disconnect the wormhole.
The sticky point I see in tonight's episode was the fact that the gate didn't draw the ship in once it was dislodged (as we've seen happen other times, as with the Russian submarine in "Watergate"). McKay figured it was because they had no inertia; it could be explained that the gate has a time limit in its systems to tell whether or not something is trying to pass through. After 37 1/2 minutes, its systems may have "forgotten" the puddle jumper and turned off the "auto-pull" feature.